It's long been believed that the Joker would one day kill Harley Quinn, but the way he finally did it when he was Emperor Joker is the opposite of what readers would expect. The relationship between the Clown Prince and Princess of Crime has been a turbulent one to say the least. The Joker has notoriously abused Harley both physically and mentally for his own personal gain. This has led to the now iconic shift in Quinn's character when she breaks off from the Joker and forms a new name for herself, instantly becoming a household name with DC Comics. However, there was a point in her comics history when Joker finally ended up killing her before she left him for good...and the reasoning behind how he does it will shock comic readers.
It all happens in the Emperor Joker storyline by Jeph Loeb. After acquiring the powers of Mister Mxyzptlk, Joker has basically acquired a god complex as he can do basically anything. One of his biggest intentions is to wipe out all of reality, which will put an end to his chaotic rule. In a way, Joker is basically seeing his unlimited power as the problem with the universe, and he sees him extinguishing all life as a way to leave "behind a clean, quiet universe." He doesn't want more people like him to have such power, so he'd rather strip it all away than risk anyone else ripping up order with unhinged chaos.
When Harley approaches him about his plan though, an unexpected side of the Joker takes form. She asks him if she really has to die too after being by his side for so long. When Joker brings her in for one last kiss, she fades from existence and turns her into a constellation in the sky, telling her this is her reward after "tears of service." It's surprisingly quick and painless for someone that has treated Harley Quinn so poorly ever since her debut in Batman: The Animated Series. In fact, it feels like she's actually honoring her rather than letting her memory fade away. This is a complete 180 from what fans usually expect from the Joker because of how sweet and memorable it is.
The way that Joker kills Harley shows that he has some type of respect for her when this is far from the truth in other iterations of the characters. This is from the man that threw her into a vat of acid to make her like him, beat her ruthlessly, left her behind to take the fall for his crimes. Seeing him have a hint of respect for her after years of his abuse just feels off. It would be more in character for him to have her feel every bit of pain just as a last laugh for himself, but he instead memorializes her before moving forward with his plan for the destruction of reality.
Of course, this isn't to say that Joker has entirely given up his looking down on Harley in this take on the character. After all, he ends up making Lois Lane his Empress, completely bypassing Quinn even after all she's done for him. Still, it's a shocking turn from what could have been when it came down to how Joker would kill her as he plots to destroy reality. The Joker could have easily made Harley Quinn's death the last laugh for himself before bringing the rest of reality with him, but instead, he does the opposite by making her a literal star, and it's a choice that is sure to leave fans baffled.